Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz

Data processed at 12:47 on 2019-08-08


Alignment Stats

Sequence pairs analysed in total 21150005
Paired-end alignments with a unique best hit 8898558
Pairs without alignments under any condition 9932657
Pairs that did not map uniquely 2318790
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 255324646
Methylated C's in CpG context 11359862
Methylated C's in CHG context 1449582
Methylated C's in CHH context 3434042
Methylated C's in Unknown context 63236
Unmethylated C's in CpG context 25363136
Unmethylated C's in CHG context 54116553
Unmethylated C's in CHH context 159601471
Unmethylated C's in Unknown context 546779
Percentage methylation (CpG context) 30.9%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 2.1%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4386310 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4512247 original bottom strand

Deduplication

Alignments analysed 8898557
Unique alignments 6392902
Duplicates removed 2505655
Duplicated alignments were found at 1529678 different positions

Cytosine Methylation after Extraction

Total C's analysed 126318223
Methylated C's in CpG context 5908942
Methylated C's in CHG context 702435
Methylated C's in CHH context 1841804
Unmethylated C's in CpG context 11618123
Unmethylated C's in CHG context 25937403
Unmethylated C's in CHH context 80309516
Percentage methylation (CpG context) 33.7%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 2.2%

M-Bias Plot